<P>
<BR>
Hi everybody,<BR>
I had run a long 100ns simulation on a tripeptide using opls/aa force field and <BR>
spc water model.<BR>
I got a few microstates.<BR>
Then I tried to run simulation on the same system using charmm force field and tip3p water <BR>
model.<BR>
However I couldn't find the microstates. Within the first 10 ns the system adopts the final<BR>
configuration that was observed in the simulation using oplsaa force field.<BR>
<BR>
<BR>
The process I used to run gromacs with charmm and tip3p water model is<BR>
<BR>
pdb2gmx -f opls.gro -ff charmm -ter -water tip3p<BR>
<BR>
charmm27-run-addtop-gromacs-dihe.sh topol.top new.top<BR>
<BR>
<BR>
mv new.top topol.top<BR>
<BR>
<BR>
#### I did modify the top file to include "tip3p-charmm.itp" <BR>
for water topology.<BR>
<BR>
<BR>
editconf -f conf.gro -o box.gro -bt cubic -d 0.75<BR>
<BR>
genbox -cs spc216.gro -cp box.gro -p topol.top -o solvated.gro<BR>
<BR>
grompp -zero -f em.mdp -c solvated.gro -o em.tpr<BR>
<BR>
<BR>
mdrun -v -s em.tpr<BR>
<BR>
<BR>
Then I generated the "tpr" file for 100ns.<BR>
<BR>
The em.mdp file includes :<BR>
<BR>
<BR>
<BR>
; User spoel (236)<BR>
; Wed Nov 3 17:12:44 1993<BR>
; Input file<BR>
;<BR>
cpp = /usr/bin/cpp<BR>
constraints = none<BR>
integrator = steep<BR>
nsteps = 100<BR>
;<BR>
; Energy minimizing stuff<BR>
;<BR>
emtol = 2000<BR>
emstep = 0.01<BR>
<BR>
<BR>
<BR>
nstcomm = 1<BR>
ns_type = grid<BR>
rlist = 1<BR>
rcoulomb = 1.0<BR>
rvdw = 1.0<BR>
Tcoupl = no<BR>
Pcoupl = no<BR>
gen_vel = no<BR>
<BR>
<BR>
The 100ns.mdp file includes:<BR>
<BR>
<BR>
;<BR>
; User spoel (236)<BR>
; Wed Nov 3 17:12:44 1993<BR>
; Input file<BR>
;<BR>
title = Yo<BR>
cpp = /usr/bin/cpp<BR>
constraints = all-bonds<BR>
integrator = md<BR>
dt = 0.002 ; ps !<BR>
nsteps = 50000000 ; total 10000 ps.<BR>
nstcomm = 1<BR>
nstxout = 250<BR>
nstvout = 1000<BR>
nstfout = 0<BR>
nstlog = 250<BR>
nstenergy = 250<BR>
nstlist = 10<BR>
ns_type = grid<BR>
rlist = 1.0<BR>
rcoulomb = 1.0<BR>
rvdw = 1.0<BR>
; Berendsen temperature coupling is on in two groups<BR>
Tcoupl = berendsen<BR>
tc-grps = Protein SOL<BR>
tau_t = 0.1 0.1<BR>
ref_t = 300 300<BR>
; Energy monitoring<BR>
energygrps = Protein SOL<BR>
; Isotropic pressure coupling is now on<BR>
Pcoupl = berendsen<BR>
Pcoupltype = isotropic<BR>
tau_p = 0.5<BR>
compressibility = 4.5e-5<BR>
ref_p = 1.0<BR>
; Generate velocites is off at 300 K.<BR>
gen_vel = no<BR>
gen_temp = 300.0<BR>
gen_seed = 173529<BR>
<BR>
<BR>
Can anyone suggest why am I not getting the microstates with "charmm " force field.<BR>
Is there anything more that I needed to do and I missed. I am sorry for such a lengthy query<BR>
<BR>
<BR>
Thanks in advance<BR>
<BR>
Sarbani<BR>
</P>
<br><br>